I created two ZIP files of the same directory. One with the GUI, the other with:
$ zip -r alpha_cmd.zip Alpha
The Alpha directory is 33.640 MB with 164 items.
The ZIP file created by the GUI is 2,100 bytes larger than the ZIP file created on the command line.
Why is the ZIP file created with the GUI larger?
Note: Even though the ZIP files have different sizes, when unzipped, each's directory has the exact same number of bytes. Basically, I'm very wary of possible inconsistencies introduced by managing my file system with the GUI and with shell commands.